Big Data Approaches to Phenotyping Acute Ischemic Stroke Using Automated Lesion Segmentation of Multi-Center Magnetic Resonance Imaging Data

Ona Wu; Stefan Winzeck; Anne-Katrin Giese; Brandon L Hancock; Mark R Etherton; Mark J R J Bouts; Kathleen Donahue; Markus D Schirmer; Robert E Irie; Steven J T Mocking; Elissa C McIntosh; Raquel Bezerra; Konstantinos Kamnitsas; Petrea Frid; Johan Wasselius; John W Cole; Huichun Xu; Lukas Holmegaard; Jordi Jiménez-Conde; Robin Lemmens; Eric Lorentzen; Patrick F McArdle; James F Meschia; Jaume Roquer; Tatjana Rundek; Ralph L Sacco; Reinhold Schmidt; Pankaj Sharma; Agnieszka Slowik; Tara M Stanne; Vincent Thijs; Achala Vagal; Daniel Woo; Stephen Bevan; Steven J Kittner; Braxton D Mitchell; Jonathan Rosand; Bradford B Worrall; Christina Jern; Arne G Lindgren; Jane Maguire; Natalia S Rost

doi:10.1161/STROKEAHA.119.025373

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Big Data Approaches to Phenotyping Acute Ischemic Stroke Using Automated Lesion Segmentation of Multi-Center Magnetic Resonance Imaging Data

Journal article

Open access

Peer reviewed

Big Data Approaches to Phenotyping Acute Ischemic Stroke Using Automated Lesion Segmentation of Multi-Center Magnetic Resonance Imaging Data

Ona Wu, Stefan Winzeck, Anne-Katrin Giese, Brandon L Hancock, Mark R Etherton, Mark J R J Bouts, Kathleen Donahue, Markus D Schirmer, Robert E Irie, Steven J T Mocking, …

Stroke (1970), Vol.50(7), pp.1734-1741

2019-07

DOI: https://doi.org/10.1161/STROKEAHA.119.025373

PMID: 31177973

Abstract

Brain Ischemia - epidemiology

Neural Networks, Computer

Stroke - diagnostic imaging

Humans

Middle Aged

Risk Factors

Big Data

Male

Machine Learning

Socioeconomic Factors

Phenotype

Algorithms

Image Processing, Computer-Assisted

Aged, 80 and over

Adult

Female

Stroke - epidemiology

Aged

Retrospective Studies

Diffusion Magnetic Resonance Imaging - methods

Brain Ischemia - diagnostic imaging

Observer Variation

Background and Purpose- We evaluated deep learning algorithms' segmentation of acute ischemic lesions on heterogeneous multi-center clinical diffusion-weighted magnetic resonance imaging (MRI) data sets and explored the potential role of this tool for phenotyping acute ischemic stroke. Methods- Ischemic stroke data sets from the MRI-GENIE (MRI-Genetics Interface Exploration) repository consisting of 12 international genetic research centers were retrospectively analyzed using an automated deep learning segmentation algorithm consisting of an ensemble of 3-dimensional convolutional neural networks. Three ensembles were trained using data from the following: (1) 267 patients from an independent single-center cohort, (2) 267 patients from MRI-GENIE, and (3) mixture of (1) and (2). The algorithms' performances were compared against manual outlines from a separate 383 patient subset from MRI-GENIE. Univariable and multivariable logistic regression with respect to demographics, stroke subtypes, and vascular risk factors were performed to identify phenotypes associated with large acute diffusion-weighted MRI volumes and greater stroke severity in 2770 MRI-GENIE patients. Stroke topography was investigated. Results- The ensemble consisting of a mixture of MRI-GENIE and single-center convolutional neural networks performed best. Subset analysis comparing automated and manual lesion volumes in 383 patients found excellent correlation (ρ=0.92; P<0.0001). Median (interquartile range) diffusion-weighted MRI lesion volumes from 2770 patients were 3.7 cm (0.9-16.6 cm ). Patients with small artery occlusion stroke subtype had smaller lesion volumes ( P<0.0001) and different topography compared with other stroke subtypes. Conclusions- Automated accurate clinical diffusion-weighted MRI lesion segmentation using deep learning algorithms trained with multi-center and diverse data is feasible. Both lesion volume and topography can provide insight into stroke subtypes with sufficient sample size from big heterogeneous multi-center clinical imaging phenotype data sets.

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.105 Strokes; 1.105.142 Stroke
Web Of Science research areas: Clinical Neurology; Peripheral Vascular Disease
ESI research areas: Neuroscience & Behavior

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Title: Big Data Approaches to Phenotyping Acute Ischemic Stroke Using Automated Lesion Segmentation of Multi-Center Magnetic Resonance Imaging Data
Creators: Ona Wu - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Stefan Winzeck - Division of Anaesthesia, Department of Medicine, University of Cambridge, United Kingdom (S.W.)
Anne-Katrin Giese - Department of Neurology, JP Kistler Stroke Research Center, MGH, Boston, MA (A.-K.G., M.R.E., K.D., M.D.S., N.S.R.)
Brandon L Hancock - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Mark R Etherton - Department of Neurology, JP Kistler Stroke Research Center, MGH, Boston, MA (A.-K.G., M.R.E., K.D., M.D.S., N.S.R.)
Mark J R J Bouts - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Kathleen Donahue - Department of Neurology, JP Kistler Stroke Research Center, MGH, Boston, MA (A.-K.G., M.R.E., K.D., M.D.S., N.S.R.)
Markus D Schirmer - Department of Neurology, JP Kistler Stroke Research Center, MGH, Boston, MA (A.-K.G., M.R.E., K.D., M.D.S., N.S.R.)
Robert E Irie - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Steven J T Mocking - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Elissa C McIntosh - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Raquel Bezerra - From Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown (O.W., S.W., B.L.H., M.J.R.J.B., R.E.I., S.J.T.M., E.C.M., R.B.)
Konstantinos Kamnitsas - Department of Computing, Imperial College London, United Kingdom (K.K.)
Petrea Frid - Department of Clinical Sciences Lund, Lund University, Sweden (P.F., J.W., A.G.L.)
Johan Wasselius - Department of Radiology (J.W.), Skåne University Hospital, Lund, Sweden
John W Cole - Department of Neurology, University of Maryland School of Medicine and Veterans Affairs Maryland Health Care System, Baltimore, MD (J.W.C., S.J.K.)
Huichun Xu - Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD (H.X., P.F.M., B.D.M.)
Lukas Holmegaard - Institute of Neuroscience and Physiology, the Sahlgrenska Academy at University of Gothenburg, Sweden (L.H.)
Jordi Jiménez-Conde - Department of Neurology, Neurovascular Research Group (NEUVAS), IMIM-Hospital del Mar (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autonoma de Barcelona, Spain (J.J.-C., J.R.)
Robin Lemmens - Department of Neurology, University Hospitals Leuven, Belgium (R.L.)
Eric Lorentzen - Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy at University of Gothenburg, Sweden (E.L., T.M.S., C.J.)
Patrick F McArdle - Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD (H.X., P.F.M., B.D.M.)
James F Meschia - Department of Neurology, Mayo Clinic, Jacksonville, FL (J.F.M.)
Jaume Roquer - Department of Neurology, Neurovascular Research Group (NEUVAS), IMIM-Hospital del Mar (Institut Hospital del Mar d'Investigacions Mèdiques), Universitat Autonoma de Barcelona, Spain (J.J.-C., J.R.)
Tatjana Rundek - Department of Neurology, Miller School of Medicine, University of Miami, The Evelyn F. McKnight Brain Institute, FL (T.R., R.L.S.)
Ralph L Sacco - Department of Neurology, Miller School of Medicine, University of Miami, The Evelyn F. McKnight Brain Institute, FL (T.R., R.L.S.)
Reinhold Schmidt - Clinical Division of Neurogeriatrics, Department of Neurology, Medical University Graz, Austria (R.S.)
Pankaj Sharma - Ashford and St Peter's Hospital, United Kingdom (P.S.)
Agnieszka Slowik - Department of Neurology, Jagiellonian University Medical College, Krakow, Poland (A.S.)
Tara M Stanne - Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy at University of Gothenburg, Sweden (E.L., T.M.S., C.J.)
Vincent Thijs - Department of Neurology, Austin Health, HDB, Australia (V.T.)
Achala Vagal - Department of Radiology (A.V.), University of Cincinnati College of Medicine, OH
Daniel Woo - Department of Neurology and Rehabilitation Medicine (D.W.), University of Cincinnati College of Medicine, OH
Stephen Bevan - School of Life Science, University of Lincoln, United Kingdom (S.B.)
Steven J Kittner - Department of Neurology, University of Maryland School of Medicine and Veterans Affairs Maryland Health Care System, Baltimore, MD (J.W.C., S.J.K.)
Braxton D Mitchell - Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, MD (B.D.M.)
Jonathan Rosand - Henry and Allison McCance Center for Brain Health Massachusetts General Hospital, Boston (J.R.)
Bradford B Worrall - Departments of Neurology and Public Health Sciences, University of Virginia, Charlottesville (B.B.W.)
Christina Jern - Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy at University of Gothenburg, Sweden (E.L., T.M.S., C.J.)
Arne G Lindgren - Department of Neurology and Rehabilitation Medicine, Neurology (A.G.L.), Skåne University Hospital, Lund, Sweden
Jane Maguire - University of Technology Sydney, Australia (J.M.)
Natalia S Rost - Department of Neurology, JP Kistler Stroke Research Center, MGH, Boston, MA (A.-K.G., M.R.E., K.D., M.D.S., N.S.R.)
Publication Details: Stroke (1970), Vol.50(7), pp.1734-1741
Publisher: United States
Grant note: R01 NS063925 / NINDS NIH HHS R01 NS030678 / NINDS NIH HHS K23 NS064052 / NINDS NIH HHS P41 EB015896 / NIBIB NIH HHS R01 NS100417 / NINDS NIH HHS P50 NS051343 / NINDS NIH HHS R01 NS039987 / NINDS NIH HHS R01 NS042733 / NINDS NIH HHS S10 RR019307 / NCRR NIH HHS U10 NS077311 / NINDS NIH HHS U01 NS069208 / NINDS NIH HHS R01 NS059775 / NINDS NIH HHS R01 NS103824 / NINDS NIH HHS R01 NS086905 / NINDS NIH HHS R01 NS082285 / NINDS NIH HHS R01 NS100178 / NINDS NIH HHS S10 RR023043 / NCRR NIH HHS S10 RR023401 / NCRR NIH HHS R01 NS029993 / NINDS NIH HHS
Academic Unit: Leadership Department; Miller School of Medicine; UMMG Department of Neurology
Language: English
Resource Type: Journal article
PMID: 31177973
Record Identifier: 991031578692402976